The Portugal captain first lifted the prize back in 2008 after leading Manchester United to the Premier League and Champions League, and joins a prestigious list of players to have been awarded the prize more than once in their career.
Messi leads the way with four Ballons d'Or to his name, with Uefa president and France icon Michel Platini level with Netherlands legends Johan Cruyff and Marco van Basten on three.
Ronaldo joins such illustrious names as former Real Madrid striker Alfredo Di Stefano, Bayern legend Franz Beckenbauer, ex-Liverpool and England star Kevin Keegan, former Germany hitman Karl-Heinz Rummenigge and Brazilian Ronaldo on two titles.
The 28-year-old, who received 27.99 per cent of the votes from national team coaches, captains and selected media representatives to win the latest award, has already set his sights on further individual glory as he aims to add to his two Ballons d'Or wins and six top-three nominations.
"Finding out I'd won made me extremely happy, I felt very proud," he told Fifa.com at the event in Zurich. "Winning a second Ballon d'Or was what I yearned for most.
"They [Platini and Pele] were truly great players in the past, great legends: it's a huge privilege to be handed this by them. I'm going to try to give my best, like I always do, and I hope to be back next year to win the third Ballon d'Or of my career. That's what I intend to do."
Ronaldo finished 2013 with a total of 69 goals in 59 appearances for club and country, including four in the crucial World Cup playoff win over Sweden in the autumn.
He set a new record for goals in the Champions League group stages, netting nine strikes in just five appearances, and was rewarded with a new contract to become the highest-paid player in Spain last September.